Alignments for a candidate for acnD in Pseudoalteromonas arctica A 37-1-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Pseudoalteromonas arctica A 37-1-2

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_007582479.1 PARC_RS10330 Fe/S-dependent 2-methylisocitrate dehydratase AcnD

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000238395.3:WP_007582479.1
          Length = 869

 Score = 1426 bits (3692), Expect = 0.0
 Identities = 706/865 (81%), Positives = 773/865 (89%), Gaps = 1/865 (0%)

Query: 1   MSTVMNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTA 60
           M+ + NTQYRKPLPG+ +DY+DT+EA++AI PGAYA LPY+SRV AENLVRRC+P MLT 
Sbjct: 1   MTIINNTQYRKPLPGSNVDYYDTQEAVDAIKPGAYATLPYSSRVFAENLVRRCDPAMLTD 60

Query: 61  SLKQIIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQL 120
           +L Q+IE KQ+LDFPW+PARVVCHDILGQTALVDLAGLRDAIAAKGGDPA+VNPVVPTQL
Sbjct: 61  ALNQLIERKQDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAKVNPVVPTQL 120

Query: 121 IVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQIN 180
           IVDHSLAVE+ GFD DAF KNRAIEDRRN+DRFHFINWT+ AFKNIDVIP GNGIMHQIN
Sbjct: 121 IVDHSLAVEHAGFDPDAFEKNRAIEDRRNDDRFHFINWTKTAFKNIDVIPPGNGIMHQIN 180

Query: 181 LERMSPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPD 240
           LE+MSPVI  R+G+AFPDTLVGTDSHTPHVDALGVIA+GVGGLEAESVMLGRASY+RLPD
Sbjct: 181 LEKMSPVIQNRDGIAFPDTLVGTDSHTPHVDALGVIAVGVGGLEAESVMLGRASYIRLPD 240

Query: 241 IIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTP 300
           I+GVELTGK QPGITATDIVLA+TEFLR Q+VVS+YLEF+GEGA+ALTLGDRATISNMTP
Sbjct: 241 IVGVELTGKRQPGITATDIVLAITEFLREQRVVSTYLEFYGEGADALTLGDRATISNMTP 300

Query: 301 EFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLS 360
           EFGATAAMFYID +T+DYL LTGRE EQ+ LVE YAKTAGLWSD LK A Y R L FDLS
Sbjct: 301 EFGATAAMFYIDDKTIDYLRLTGREEEQIALVENYAKTAGLWSDSLKTAKYERVLKFDLS 360

Query: 361 SVVRTIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVI 420
           SV R IAGPSNPH RV TS+LA  GISG VENE GLMPDGA IIAAITSCTNTSNPRNVI
Sbjct: 361 SVGRNIAGPSNPHRRVSTSDLAKEGISGVVENEEGLMPDGACIIAAITSCTNTSNPRNVI 420

Query: 421 AAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCN 480
           AA LLARNANAKGL RKPWVKTSLAPGSKAVQ YLE+ANLL ELE LGFGIVGFACTTCN
Sbjct: 421 AAALLARNANAKGLMRKPWVKTSLAPGSKAVQSYLEDANLLTELEQLGFGIVGFACTTCN 480

Query: 481 GMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIR 540
           GMSGALDPVIQ+EVIDRDLY TAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIR
Sbjct: 481 GMSGALDPVIQKEVIDRDLYTTAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIR 540

Query: 541 FDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKV 600
           FDIEK +LG D+ G  + L ++WPSD EIDAVI  SVKPEQFRKVYEPMF+L+VDYG+  
Sbjct: 541 FDIEKGILGQDQQGNDITLKDLWPSDEEIDAVIKQSVKPEQFRKVYEPMFNLTVDYGEDN 600

Query: 601 SPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAG 660
            PLYDWRP+STYIRRPPYWEGALAGERT+ GMR LAVLGDNITTDHLSPSNAIM  SAAG
Sbjct: 601 DPLYDWRPESTYIRRPPYWEGALAGERTMTGMRALAVLGDNITTDHLSPSNAIMASSAAG 660

Query: 661 EYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAI-VDGKVKQGSLARIEPEG 719
           EYL KM +PEED+NSYATHRGDHLTAQRATFANPKL NEM +  +G+VKQGS AR+EP+G
Sbjct: 661 EYLTKMNVPEEDYNSYATHRGDHLTAQRATFANPKLLNEMVLDENGEVKQGSYARLEPQG 720

Query: 720 IVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTN 779
             TRMWEAIE YM+RKQPLII+AGADYGQGSSRDWAAKGVRLAGVE I AEGFERIHRTN
Sbjct: 721 TNTRMWEAIEAYMERKQPLIIVAGADYGQGSSRDWAAKGVRLAGVEVIAAEGFERIHRTN 780

Query: 780 LVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRL 839
           L+GMGVLPLEFKAG  R T  +DG+E +DV G + P A + + ITRK+GE + VP+ CR+
Sbjct: 781 LIGMGVLPLEFKAGTTRKTLELDGSETYDVSGDLKPGATVNLSITRKDGEVLTVPMKCRI 840

Query: 840 DTAEEVSIYEAGGVLQRFAQDFLES 864
           DT EE+SIY AGGVLQRFAQDFLE+
Sbjct: 841 DTQEELSIYAAGGVLQRFAQDFLEA 865


Lambda     K      H
   0.318    0.136    0.397 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 2217
Number of extensions: 93
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 867
Length of database: 869
Length adjustment: 42
Effective length of query: 825
Effective length of database: 827
Effective search space:   682275
Effective search space used:   682275
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources